Synthetic biology can be broadly broken down into the ‘top-down’ synthesis of genomes (Gibson, et al., Science (2010) 329:52-56) and the ‘bottom-up’ engineering of relatively small genetic circuits (Hasty, et al., Nature (2001) 420:224-230 (2002); Sprinzak, et al., Nature 438:443-448 (2005); Endy, Nature (2005) 438:449-453; Ellis, et al., Nature Biotechnol. (2009) 27:465-471; Kobayashi, et al. Proc. Natl Acad. Sci. USA (2004) 101: 8414-8419; You, et al., Nature (2004) 428:868-871; Basu, et al., Nature (2005) 434:1130-1134; Mukherji, et al., Nature Rev. Genet. 10:859-871; Grilly, et al., Mol. Syst. Biol. (2007) 3:127). In the field of genetic circuits, toggle switches (Gardner, et al., Nature (2000) 403:339-342) and oscillators (Elowitz, et al., Nature (2000) 403, 335-338) have progressed into triggers (Lu, et al., Proc. Natl Acad. Sci. USA 104:11197-11202), counters (Friedland, et al., Science (2009) 324:1199-1202) and synchronized clocks (Danino, et al., Nature (2010) 463:326-330). Sensors have arisen as a major focus in the context of biotechnology (Kobayashi, et al. Proc. Natl Acad. Sci. USA (2004) 101: 8414-8419; Tamsir, et al., Nature (2011) 469:212-215; Tabor, et al., Cell (2009) 137:1272-1281), while oscillators have provided insights into the basic-science functionality of cyclic regulatory processes (Stricker, et al., Nature (2008) 456:516-519; Mondragon-Palomino, et al., Science (2011) 333:1315-1319; Tigges, et al., Nature (2009) 457:309-312). A common theme is the concurrent development of mathematical modelling that can be used for experimental design and characterization, as in physics and the engineering disciplines.
The synchronization of genetic clocks provides a particularly attractive avenue for synthetic biology applications. Oscillations permeate science and technology in a number of disciplines, with familiar examples including alternating current (AC) power (U.S. Pat. No. 373,035), the global positioning system (GPS) (Lewandowski, et al., Proc. IEEE (1999) 87:163-172) and lasers (Vladimirov, et al., Europhys. Lett. (2003) 61:613). These technologies have demonstrated that operating in the frequency domain can offer considerable advantages over steady-state designs in terms of information gathering and transmission. In particular, oscillatory sensors confer a number of advantages to traditional ones (Gast, J. Phys. E: Sci. Instrum. (1985) 18:783), as frequency is easily digitized and can be quickly updated with repeated measurements. For sensors that use optical reporters, measurements of frequency are less sensitive to experimental factors such as beam power and exposure time than intensity measurements, which must be normalized and calibrated.
Although the bottom-up approach to synthetic biology is increasingly benefiting from DNA synthesis technologies, the general design principles are still evolving. In this context, a substantial challenge is the construction of robust circuits in a cellular environment that is governed by noisy processes such as random bursts of transcription and translation (Ozbudak, et al., Nature Genet. (2002) 31:69-73; Elowitz, et al., Science (2002) 297:1183-1186; Golding, et al., Cell (2005) 123:1025-1036; Blake, et al., Mol. Cell (2006) 24:853-865; Austin, et al. Nature (2006) 439:608-611). Such an environment leads to considerable inter-cellular variability in circuit behavior, which can impede coherent functionality at the colony level. An ideal design strategy for reducing variability across a cellular population would involve both strong and long-range coupling that would instantaneously synchronize the response of millions of cells. Quorum sensing typically involves strong intercellular coupling over tens of micrometers (Basu, et al., Nature (2005) 434:1130-1134; Danino, et al., Nature (2010) 463:326-330; Waters, et al., Annu. Rev. Cell Dev. Biol. (2005) 21:319-346), yet the relatively slow diffusion time of molecular communication through cellular media leads to signalling delays over millimeter scales. Faster communication mechanisms, such as those mediated in the gas or vapor phase, may increase the length scale for instantaneous communication, but are comparatively weak and short lived because the vapor species more readily disperse.